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Assembly: a resource for assembled genomes at NCBI
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.tig.2014.07.001openalex-snapshot
Ten years of next-generation sequencing technology
inferredcites →https://doi.org/10.1038/ncomms2192openalex-snapshot
Genome sequences of wild and domestic bactrian camels
inferredcites →https://doi.org/10.1038/ncomms3445openalex-snapshot
Draft genome sequence of the mulberry tree Morus notabilis
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/nar/gkr1163openalex-snapshot
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
inferredcites →https://doi.org/10.1093/nar/gkt1076openalex-snapshot
Data, information, knowledge and principle: back to metabolism in KEGG
inferredcites →https://doi.org/10.1093/nar/gku950openalex-snapshot
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
inferredcites →https://doi.org/10.1093/nar/gku990openalex-snapshot
diArk – the database for eukaryotic genome and transcriptome assemblies in 2014
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1101/gr.180893.114openalex-snapshot
Single haplotype assembly of the human genome from a hydatidiform mole
inferredcites →https://doi.org/10.1126/science.1252806openalex-snapshot
The sheep genome illuminates biology of the rumen and lipid metabolism
inferredcites →https://doi.org/10.1186/1471-2164-15-578openalex-snapshot
Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha
inferredcites →https://doi.org/10.1186/s12864-015-1294-xopenalex-snapshot
Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis
inferredcites →https://doi.org/10.1186/s13059-014-0466-3openalex-snapshot
Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment
inferredcites →https://doi.org/10.1371/journal.pbio.1001091openalex-snapshot
Modernizing Reference Genome Assemblies
inferredcites →https://doi.org/10.1371/journal.pbio.1002005openalex-snapshot
The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
inferredcites →https://doi.org/10.3389/fcimb.2013.00065openalex-snapshot
Fungal zinc metabolism and its connections to virulence
inferredcites →https://doi.org/10.4056/sigs.4851102openalex-snapshot
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A Comprehensive Analysis of the Global Human Gut Archaeome from a Thousand Genome Catalogue
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Calcium‐Dependent Lipopeptide Antibiotics against Drug‐Resistant Pathogens Discovered via Host‐Dependent Heterologous Expression of a Cloned Biosynthetic Gene Cluster
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Genome Annotation and Analysis
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Genome-scale metabolic models enable predictive strain and process design for sustainable biomanufacturing
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Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes
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Pitfalls of genotyping microbial communities with rapidly growing genome collections
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The impacts of 2,4-D herbicide DMA® 4 IVM on reproductive health and gene expression along the hypothalamic-pituitary-gonad-liver [HPGL] axis in the fathead minnow (Pimephales promelas)
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Systems-level analysis prioritizes the importance of IFNG, SULF1, and OAS3 genes in head and neck cancer
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Phenotype databases for genetic screens in human cells
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Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation
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The epidemiology and hypervirulence of Klebsiella pneumoniae ST23 unveil epidemic risks in China and worldwide
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AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes
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Distribution and molecular profile of betaine lipids in basidiomycete fungi
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Metagenomic insights into the diet and past Kolyma Lowland habitat from the intestinal content of a Late Pleistocene steppe bison
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Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex
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Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations
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Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes
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Functional Characterization of Cj1427, a Unique Ping-Pong Dehydrogenase Responsible for the Oxidation of GDP- d -glycero-α- d -manno-heptose in Campylobacter jejuni
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Biosynthesis of GDP- d -glycero-α- d -manno-heptose for the Capsular Polysaccharide of Campylobacter jejuni
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Unsupervised Machine Learning Organization of the Functional Dark Proteome of Gram-Negative “Superbugs”: Six Protein Clusters Amenable for Distinct Scientific Applications
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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing
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Narrow-spectrum resource-utilizing bacteria drive the stability of synthetic communities through enhancing metabolic interactions
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Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae
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DiscERN: an automated genome mining tool for the discovery of evolutionarily related natural products
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Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics
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Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome
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A catalogue of 1,167 genomes from the human gut archaeome
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A complete domain-to-species taxonomy for Bacteria and Archaea
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A unified catalog of 204,938 reference genomes from the human gut microbiome
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Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease
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Efficient and robust search of microbial genomes via phylogenetic compression
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Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering
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A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota
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Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
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Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens
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The evolutionary landscape of prokaryotic chromosome/plasmid balance
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PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics
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Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments
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Genome wide characterization of IDZ gene family in Arabidopsis thaliana and Triticum aestivum checking the response of TaIDZ genes against cold stress
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Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons
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Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation
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RNA aptamers for sodium and lithium are abundant in mammals
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The enigmatic RNase MRP of kinetoplastids
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Genome-wide identification and expression analysis of the CHYR gene family in Phaseolus vulgaris under abiotic stress at the seeding stage
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Propagation, detection and correction of errors using the sequence database network
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FAIR Header Reference genome: a TRUSTworthy standard
inferred← citeshttps://doi.org/10.1093/bib/bbag357openalex-snapshot
Genome assemblies and annotations are not static and need support for tracking their evolution
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab855openalex-snapshot
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
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BinDash, software for fast genome distance estimation on a typical personal laptop
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
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An integrated culturomic and genomic database and analysis platform for methanogenic archaea
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Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata
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Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade
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Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud)
inferred← citeshttps://doi.org/10.1093/femsec/fiag063openalex-snapshot
Metabolism of β -mannans by representative, understudied Bacillota species from the human colon
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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
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Rapid divergence of the male reproductive proteins in the Drosophila dunni group and implications for postmating incompatibilities between species
inferred← citeshttps://doi.org/10.1093/g3journal/jkab181openalex-snapshot
Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
inferred← citeshttps://doi.org/10.1093/gbe/evab165openalex-snapshot
Genome-Wide Detection of Structural Variations Reveals New Regions Associated with Domestication in Small Ruminants
inferred← citeshttps://doi.org/10.1093/gbe/evab213openalex-snapshot
Microbial Phylogenetic Context Using Phylogenetic Outlines
inferred← citeshttps://doi.org/10.1093/gbe/evad156openalex-snapshot
Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales
inferred← citeshttps://doi.org/10.1093/gbe/evae019openalex-snapshot
Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification
inferred← citeshttps://doi.org/10.1093/gbe/evz274openalex-snapshot
Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes
inferred← citeshttps://doi.org/10.1093/gigascience/giad080openalex-snapshot
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
inferred← citeshttps://doi.org/10.1093/gigascience/giae081openalex-snapshot
Genomic exploration of the endangered oriental stork, Ciconia boyciana , sheds light on migration adaptation and future conservation
inferred← citeshttps://doi.org/10.1093/gigascience/giaf003openalex-snapshot
Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin
inferred← citeshttps://doi.org/10.1093/gigascience/giag024openalex-snapshot
HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification
inferred← citeshttps://doi.org/10.1093/gigascience/giy017openalex-snapshot
G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences
inferred← citeshttps://doi.org/10.1093/gigascience/giz149openalex-snapshot
Refgenie: a reference genome resource manager
inferred← citeshttps://doi.org/10.1093/icb/icaa138openalex-snapshot
Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird
inferred← citeshttps://doi.org/10.1093/ismeco/ycaf167openalex-snapshot
Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil
inferred← citeshttps://doi.org/10.1093/mmy/myae053openalex-snapshot
Prevalence and genetic diversity of azole-resistant Malassezia pachydermatis isolates from canine otitis and dermatitis: A 2-year study
inferred← citeshttps://doi.org/10.1093/molbev/msab094openalex-snapshot
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species
inferred← citeshttps://doi.org/10.1093/molbev/msae088openalex-snapshot
Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota
inferred← citeshttps://doi.org/10.1093/nar/gkaa1105openalex-snapshot
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
inferred← citeshttps://doi.org/10.1093/nar/gkaa1195openalex-snapshot
Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome
inferred← citeshttps://doi.org/10.1093/nar/gkab1136openalex-snapshot
IMGT® databases, related tools and web resources through three main axes of research and development
inferred← citeshttps://doi.org/10.1093/nar/gkab776openalex-snapshot
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
inferred← citeshttps://doi.org/10.1093/nar/gkac301openalex-snapshot
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
inferred← citeshttps://doi.org/10.1093/nar/gkac963openalex-snapshot
KEGG for taxonomy-based analysis of pathways and genomes
inferred← citeshttps://doi.org/10.1093/nar/gkad875openalex-snapshot
gcPathogen: a comprehensive genomic resource of human pathogens for public health
inferred← citeshttps://doi.org/10.1093/nar/gkad946openalex-snapshot
ViralZone 2024 provides higher-resolution images and advanced virus-specific resources
inferred← citeshttps://doi.org/10.1093/nar/gkad987openalex-snapshot
The UCSC Genome Browser database: 2024 update
inferred← citeshttps://doi.org/10.1093/nar/gkaf1040openalex-snapshot
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
inferred← citeshttps://doi.org/10.1093/nar/gkag133openalex-snapshot
Diversity and distribution of bacterial DNA polymerases
inferred← citeshttps://doi.org/10.1093/nar/gkag975openalex-snapshot
Fast, flexible gene cluster family delineation with IGUA
inferred← citeshttps://doi.org/10.1093/nar/gkv1290openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gkv1356openalex-snapshot
The 2016 database issue ofNucleic Acids Researchand an updated molecular biology database collection
inferred← citeshttps://doi.org/10.1093/nar/gkw1071openalex-snapshot
Database Resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gkw1131openalex-snapshot
CyanoBase: a large-scale update on its 20th anniversary
inferred← citeshttps://doi.org/10.1093/nar/gkw343openalex-snapshot
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
inferred← citeshttps://doi.org/10.1093/nar/gkw903openalex-snapshot
World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide
inferred← citeshttps://doi.org/10.1093/nar/gky1069openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gky212openalex-snapshot
riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
inferred← citeshttps://doi.org/10.1093/nar/gkz894openalex-snapshot
PmiREN: a comprehensive encyclopedia of plant miRNAs
inferred← citeshttps://doi.org/10.1093/nar/gkz899openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nargab/lqab036openalex-snapshot
Identity and compatibility of reference genome resources
inferred← citeshttps://doi.org/10.1093/nargab/lqaf127openalex-snapshot
IMGT® analysis of the human IGH locus: unveiling novel polymorphisms and copy number variations in 15 genome assemblies from diverse ancestral backgrounds
inferred← citeshttps://doi.org/10.1093/nargab/lqaf141openalex-snapshot
Quantifying annotation-driven bias in alternative splicing from EGAP metadata
inferred← citeshttps://doi.org/10.1093/nargab/lqag020openalex-snapshot
Unraveling IGK locus in dog breeds: IMGT® new insights into canine immunogenetics
inferred← citeshttps://doi.org/10.1093/pcp/pcae083openalex-snapshot
Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 6803
inferred← citeshttps://doi.org/10.1093/ve/veab012openalex-snapshot
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes
inferred← citeshttps://doi.org/10.1093/ve/veac085openalex-snapshot
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae )
inferred← citeshttps://doi.org/10.1096/fj.202302423rropenalex-snapshot
Biosensor capability of the endometrium is mediated in part, by altered miRNA cargo from conceptus‐derived extracellular vesicles
inferred← citeshttps://doi.org/10.1098/rstb.2020.0157openalex-snapshot
MolluscDB: a genome and transcriptome database for molluscs
inferred← citeshttps://doi.org/10.1099/acmi.0.000796.v3openalex-snapshot
Draft genome sequence of a Lactiplantibacillus pentosus strain isolated from traditionally fermented rice
inferred← citeshttps://doi.org/10.1099/acmi.0.001085.v3openalex-snapshot
Seventeen complete genome assemblies to augment sequencing coverage of bacterial plant pathogens in the UK Plant Health Risk Register
inferred← citeshttps://doi.org/10.1099/ijsem.0.005428openalex-snapshot
Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea
inferred← citeshttps://doi.org/10.1099/ijsem.0.006514openalex-snapshot
Streptomyces castrisilvae sp. nov. and Streptomyces glycanivorans sp. nov., novel soil streptomycetes metabolizing mutan and alternan
inferred← citeshttps://doi.org/10.1099/ijsem.0.006733openalex-snapshot
Taxonomic revision of the family Aurantimonadaceae: proposal of Dennerimonas gen. nov., Mesocryomonas gen. nov., Rathsackimonas gen. nov. and Plantimonas gen. nov., along with the reclassification of Jeongeupella Jiang et al. 2024 as a later heterotypic synonym of Antarcticirhabdus Du et al. 2023
inferred← citeshttps://doi.org/10.1099/ijsem.0.006809openalex-snapshot
Taxonomic rearrangement of Salinibacterium, Leifsonia, Diaminobutyricibacter, Antiquaquibacter, Homoserinimonas and Glaciibacter: refining genus boundaries and proposal of two new genera – Orlajensenia gen. nov. and Leifsonella gen. nov.
inferred← citeshttps://doi.org/10.1099/mgen.0.000309openalex-snapshot
Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation
inferred← citeshttps://doi.org/10.1099/mgen.0.000770openalex-snapshot
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes
inferred← citeshttps://doi.org/10.1099/mgen.0.000858openalex-snapshot
Shooting hoops: globetrotting plasmids spreading more than just antimicrobial resistance genes across One Health
inferred← citeshttps://doi.org/10.1099/mgen.0.001206openalex-snapshot
A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex
inferred← citeshttps://doi.org/10.1099/mgen.0.001457openalex-snapshot
Genomic diversity and functional insights of carbapenem-resistant Klebsiella pneumoniae revealed by centroid coding sequences analysis
inferred← citeshttps://doi.org/10.1099/mgen.0.001633openalex-snapshot
Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa
inferred← citeshttps://doi.org/10.1101/067447openalex-snapshot
High-Quality Assembly of an Individual of Yoruban Descent
inferred← citeshttps://doi.org/10.1101/2020.03.20.999532openalex-snapshot
Insights on the taxonomy and ecogenomics of the Synechococcus collective
inferred← citeshttps://doi.org/10.1101/2020.10.10.334193openalex-snapshot
Features of Functional Human Genes
inferred← citeshttps://doi.org/10.1101/2020.10.16.342287openalex-snapshot
Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
inferred← citeshttps://doi.org/10.1101/2021.06.24.449536openalex-snapshot
Elucidating the genome of Emydura subglobosa through manual annotation and computational biology tools
inferred← citeshttps://doi.org/10.1101/2021.08.20.457063openalex-snapshot
Evolutionary history of mammalian UDP-glucuronosyltransferase (UGT)1 and UGT2 families: the emergence of UGT2B subfamily in eutherians after the diversification of flowering plants
inferred← citeshttps://doi.org/10.1101/2021.10.26.465843openalex-snapshot
Diversity, function and evolution of marine microbe genomes
inferred← citeshttps://doi.org/10.1101/2021.11.11.468318openalex-snapshot
Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets
inferred← citeshttps://doi.org/10.1101/2022.05.15.492003openalex-snapshot
Hecatomb: An End-to-End Research Platform for Viral Metagenomics
inferred← citeshttps://doi.org/10.1101/2022.06.14.496215openalex-snapshot
AuCoMe: inferring and comparing metabolisms across heterogeneous sets of annotated genomes
inferred← citeshttps://doi.org/10.1101/2022.09.21.508815openalex-snapshot
From motor protein to toxin: Mutations in the zonula occludens toxin (Zot) of Vibrio cholerae phage CTXϕ suggest a loss of phage assembly function
inferred← citeshttps://doi.org/10.1101/2023.06.22.546130openalex-snapshot
Early divergence and gene exchange highways in the evolutionary history of Mesoaciditogales
inferred← citeshttps://doi.org/10.1101/2023.10.17.562709openalex-snapshot
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’
inferred← citeshttps://doi.org/10.1101/2023.10.22.563459openalex-snapshot
The accuracy of Apis mellifera reference genomes: from version Amel 3.0 to Amel 4.5
inferred← citeshttps://doi.org/10.1101/2023.12.20.572685openalex-snapshot
A community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance
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